Hi Jieqiu Yang
There could be many sources of interrupts that could wakeup the MCU as long as any interrupt could wakeup the MCU;
Did the GPIO interrupt is the only one configured before your MCU goes to VLPS mode? I would recommend to isolate the issue by disabling all other possible interrupts and check if it is your GPIO interrupt or there is other source for the problem.
I would also recommend to check the noise level in the pin that wakeup your MCU, if it is high, it could be the one that wake up your MCU.
Also, the NMI interrupt could be being triggered, did you have an external pull up resistor in this pin?
Hope this information could help you.
Best Regards.